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- PDB-5byl: Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5byl | ||||||
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Title | Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH(2'')-Ia) in complex with GMPPCP and Magnesium | ||||||
![]() | Bifunctional AAC/APH | ||||||
![]() | TRANSFERASE / Kinase / Antibiotic / Aminoglycoside / Resistance | ||||||
Function / homology | ![]() aminoglycoside phosphotransferase activity / aminoglycoside 2''-phosphotransferase / N-acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Caldwell, S.J. / Berghuis, A.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Antibiotic Binding Drives Catalytic Activation of Aminoglycoside Kinase APH(2)-Ia. Authors: Caldwell, S.J. / Huang, Y. / Berghuis, A.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 538.4 KB | Display | ![]() |
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PDB format | ![]() | 442.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5iqaC ![]() 5iqbC ![]() 5iqcC ![]() 5iqdC ![]() 5iqeC ![]() 5iqfC ![]() 5iqgC ![]() 5iqhC ![]() 5iqiC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Details | SAXS |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 35948.199 Da / Num. of mol.: 4 / Fragment: C-terminal domain (UNP residues 175-479) Source method: isolated from a genetically manipulated source Details: C-terminal domain of AAC(6')-Ie/APH(2'')-Ia bifunctional enzyme, residues 175-479 Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A0C1, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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-Non-polymers , 5 types, 1081 molecules ![](data/chem/img/GCP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GCP / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.62 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 80-120mM MgCl2, 8% Glycerol, 10% PEG3350, 100mM HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Nov 26, 2013 |
Radiation | Monochromator: ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→58.92 Å / Num. obs: 82837 / % possible obs: 95 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.091 / Net I/av σ(I): 3.8 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.6 / % possible all: 65.6 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: APH(2'')-Ia GMPPNP-Mg complex Resolution: 2.15→58.92 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Authors state that MG 700 and GCP 500 of chain C have a clash that appears to be a consequence of multiple discrete states in the active site. Refinement of multiple occupancy MG 700 ...Details: Authors state that MG 700 and GCP 500 of chain C have a clash that appears to be a consequence of multiple discrete states in the active site. Refinement of multiple occupancy MG 700 diverged from physiologically sensible positions, and so the single occupancy was retained, despite this clash.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.77 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→58.92 Å
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Refine LS restraints |
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